Both LilyPond and ABC are already supported through the Score extension, but cannot be uploaded to Commons or rendered as thumbnails. The LilyPond software does have the ability to export to other formats, such as PDF and SVG. (Currently the extension renders scores as PNG and not as SVG; see T49578.)
There is no requirement to enable thumbnails or playback before it becomes possible to upload files to Commons; there was (I think) no expectation in the RfC that this would occur immediately due to the Community Wishlist Survey proposal for such not reaching the top 10.
Both LilyPond and ABC scores are intended to be written directly as source code. I don't know if this would cause security or upload issues.